GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1179997

Query DataSets for GSM1179997

Status

Public on Aug 31, 2013

Title

Wild-type rice leaves replicate 3

Sample type

RNA

Source name

Wild-type rice leaves

Organism

Oryza sativa

Characteristics

genotype/variation: Wild-type rice leaves

Treatment protocol

Fourth leaves were harvested from WT, OsWRKY53-overexpressing rice plants and OsWRKY53SD-overexpressing rice plants at the four-leaf stage.

Growth protocol

Rice plants were grown in a chamber under a 14-h-light (28℃) and 10-h-dark (24℃) cycle in hydroponic culture.

Extracted molecule

total RNA

Extraction protocol

RNeasy Plant Mini Kit (Qiagen)

Label

Cy3

Label protocol

Low RNA input Linear Amplification/Labeling Kit (Agilent)

Hybridization protocol

Agilent protocol G4140-90040

Scan protocol

Agilent scanner model G2565

Description

Biological replicate 3 of 4.

Data processing

After data was analyzed by Fearure Extraction software (version 11, Agilent), data normalization was performed using Partek Genomics Suite software (ver. 6.5; Partek software) by quantile normalization method.

Submission date

Jul 02, 2013

Last update date

Nov 04, 2013

Contact name

Kazunori Okada

E-mail(s)

ukokada@mail.ecc.u-tokyo.ac.jp

Phone

+81-3-5841-3070

Organization name

The University of Tokyo

Department

Biotechnology Research Center

Lab

Laboratory of Environmental Biochemistry

Street address

1-1-1, Yayoi, Bunkyo-ku

City

Tokyo

ZIP/Postal code

113-8657

Country

Japan

Platform ID

GPL8852

Series (1)

GSE48500

Effect of overexpression of the OsWRKY53 or phospho-mimicking mutant of OsWRKY53 in rice

Data table header descriptions
ID_REF
VALUE	Normalized signal intensity (log 2)

Data table
ID_REF	VALUE
Os01g0100100\|COMBINER_EST\|CI448596\|0	11.0527
Os01g0100200\|mRNA\|AK059894\|CDS+3'UTR	2.43028
Os01g0100400\|mRNA\|AK101455\|CDS+3'UTR	6.2527
Os01g0100500\|mRNA\|AK067316\|CDS+3'UTR	12.1288
Os01g0100600\|mRNA\|AK121362\|CDS+3'UTR	11.6629
Os01g0100700\|mRNA\|AK059844\|CDS+3'UTR	13.9332
Os01g0100700\|mRNA\|AK121523\|CDS+3'UTR	11.9703
Os01g0100800\|mRNA\|AK122012\|CDS+3'UTR	11.0381
Os01g0100900\|COMBINER_EST\|CI015509\|0	12.3782
Os01g0101200\|mRNA\|AK067866\|CDS+3'UTR	12.3753
Os01g0101200\|mRNA\|AK104517\|CDS+3'UTR	14.885
Os01g0101200\|mRNA\|AK104625\|CDS+3'UTR	15.0549
Os01g0101200\|mRNA\|AK104752\|CDS+3'UTR	14.9627
Os01g0101200\|mRNA\|AK119457\|CDS+3'UTR	9.15202
Os01g0101300\|COMBINER_EST\|CI016681\|6	10.0579
Os01g0101600\|mRNA\|AK099952\|CDS+3'UTR	5.2416
Os01g0101600\|mRNA\|AK103820\|CDS+3'UTR	12.0296
Os01g0101600\|mRNA\|AK122118\|CDS+3'UTR	12.1093
Os01g0101700\|COMBINER_EST\|CI525185\|3	14.4047
Os01g0101800\|mRNA\|AK103498\|CDS+3'UTR	10.8987

Total number of rows: 42477

Table truncated, full table size 1848 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1179997_US90500268_251524114281_S01_GE1_105_Dec08_1_1.txt.gz	7.7 Mb	(ftp)(http)	TXT
Processed data included within Sample table